Bug in pval computation

[zachalexan]

Hello,

I am having difficulty retrieving pvals when method='amoc'.

Looking at this chunk (lines 92-97 in EDM.R):

            over = 1
            for(i in 1:nperm){
                Zcounts = sample(Zcounts)
                stat = Analysis(Zcounts, min.size, alpha)
                if(stat$stat >= retList$stat)
                    over = over + 1

I don't believe retList has been initialized. So stat$stat >= retList$stat is always false. Indeed,
running breakout with nperm=N results in a p-value of 1/(N+1).

Forgive me if I'm pointing out something incorrect or already known. I couldn't find any mention of it here.

[zachalexan]

Spoke too soon. I see where retList is initialized, but the fact remains that the p-value is always 1/(N+1)